6KSF

Crystal Structure of ALKBH1 bound to 21-mer DNA bulge

Summary for 6KSF

• Entry DOI: 10.2210/pdb6ksf/pdb
• Descriptor: Alpha-ketoglutarate-dependent dioxygenase alkB homolog 1, DNA (5'-D(*DGP*DCP*DTP*DGP*DAP*DGP*DTP*DGP*DCP*DCP*DCP*DGP*DCP*DGP*DTP*DGP*DCP*DTP*DGP*DGP*DAP*DTP*DCP*DC)-3'), DNA (5'-D(*DGP*DGP*DAP*DTP*DCP*DCP*DAP*DGP*DCP*DAP*DCP*DGP*DCP*DCP*DAP*DCP*DTP*DCP*DAP*DGP*DC)-3'), ... (7 entities in total)
• Functional Keywords: dna methylation, complex, demethylase, gene regulation
• Biological source: Mus musculus (house mouse); More
• Total number of polymer chains: 3
• Total formula weight: 52109.35

Authors

Li, H.,Zhang, M. (deposition date: 2019-08-23, release date: 2020-04-08, Last modification date: 2024-10-23)

Primary citation

Zhang, M.,Yang, S.,Nelakanti, R.,Zhao, W.,Liu, G.,Li, Z.,Liu, X.,Wu, T.,Xiao, A.,Li, H.
Mammalian ALKBH1 serves as an N6-mA demethylase of unpairing DNA.
Cell Res., 30:197-210, 2020

PubMed Abstract: N-methyladenine (N-mA) of DNA is an emerging epigenetic mark in mammalian genome. Levels of N-mA undergo drastic fluctuation during early embryogenesis, indicative of active regulation. Here we show that the 2-oxoglutarate-dependent oxygenase ALKBH1 functions as a nuclear eraser of N-mA in unpairing regions (e.g., SIDD, Stress-Induced DNA Double Helix Destabilization regions) of mammalian genomes. Enzymatic profiling studies revealed that ALKBH1 prefers bubbled or bulged DNAs as substrate, instead of single-stranded (ss-) or double-stranded (ds-) DNAs. Structural studies of ALKBH1 revealed an unexpected "stretch-out" conformation of its "Flip1" motif, a conserved element that usually bends over catalytic center to facilitate substrate base flipping in other DNA demethylases. Thus, lack of a bending "Flip1" explains the observed preference of ALKBH1 for unpairing substrates, in which the flipped N-mA is primed for catalysis. Co-crystal structural studies of ALKBH1 bound to a 21-mer bulged DNA explained the need of both flanking duplexes and a flipped base for recognition and catalysis. Key elements (e.g., an ALKBH1-specific α1 helix) as well as residues contributing to structural integrity and catalytic activity were validated by structure-based mutagenesis studies. Furthermore, ssDNA-seq and DIP-seq analyses revealed significant co-occurrence of base unpairing regions with N-mA in mouse genome. Collectively, our biochemical, structural and genomic studies suggest that ALKBH1 is an important DNA demethylase that regulates genome N-mA turnover of unpairing regions associated with dynamic chromosome regulation.

PubMed: 32051560
DOI: 10.1038/s41422-019-0237-5

Experimental method

X-RAY DIFFRACTION (2.4 Å)